[BioC] error in coverting readaligned object to GenomeData

[Martin Morgan]

Hi Andreia --

On 07/18/2011 11:04 AM, Andreia Fonseca wrote:
> Dear all,
>
> I am newby in analysing chip-seq data and I am getting an error in coverting
> my readaligned object to a GenomeData object
>
> the commands that I am using are:
> library(ShortRead)
> library(PICS)
> library(ChIPpeakAnno)
> library(snowfall)
> exDir<-("/RAID/Paula_chip_seq_data/")
>
> dataIP_JKA<-readAligned(dirPath=exDir, type="Bowtie",
> pattern="110402_SN365_B_s_2_seq_GQG-1")
> dataIP_JKA<- as(dataIP_JKA, "GenomeData")
>
> Error in as.list.default(from) :
>    no method for coercing this S4 class to a vector
> In addition: Warning message:
> Storing reads only by their start positions is deprecated. Please use a
> range representation like GRanges.

I'm not sure where you're getting the instructions to coerce to a 
'GenomicData' object, but these are no longer supported. For a 
reproducible example, I ran

   library(ShortRead)
   example(readAligned)

and then

   as(aln2, "GRanges")

But likely you'll want to (a) get Bowtie to export sam or bam files and 
(b) use GenomicRanges::readGappedAlignments to read the aligned data. 
This will be a much smaller object, and already closer to the format 
you're interested in.

>> dataCont_JKA
> class: AlignedRead
> length: 6443227 reads; width: 50 cycles
> chromosome: chr20 chr17 ... chr8 chr21
> position: 41162388 77764636 ... 59583233 34102674
> strand: - - ... - +
> alignQuality: NumericQuality
> alignData varLabels: similar mismatch
>
>
> I  am getting also an error when trying to convert the map file into a
> RangeData object
>
> map<-read.table("/RAID/Paula_chip_seq_data/hg19.fa-50.bed", header =
> TRUE,colClasses = c("factor", "integer", "integer", "NULL"))
>> map<- as(map, "RangedData")

here I think you want to use rtracklayer::import().

Martin

>
> thanks for the help.
> Andreia
>
>
>
> sessionInfo()
> R version 2.13.1 (2011-07-08)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>   [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
>   [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>   [1] snowfall_1.84                       snow_0.3-5
>   [3] ChIPpeakAnno_1.8.0                  limma_3.8.2
>   [5] org.Hs.eg.db_2.5.0                  GO.db_2.4.1
>   [7] RSQLite_0.9-1                       DBI_0.2-5
>   [9] AnnotationDbi_1.14.1                BSgenome.Ecoli.NCBI.20080805_1.3.17
> [11] multtest_2.8.0                      Biobase_2.12.2
> [13] biomaRt_2.8.1                       PICS_1.6.0
> [15] BSgenome_1.20.0                     ShortRead_1.10.4
> [17] Rsamtools_1.4.2                     lattice_0.19-30
> [19] Biostrings_2.20.1                   GenomicRanges_1.4.6
> [21] IRanges_1.10.4
>
> loaded via a namespace (and not attached):
> [1] grid_2.13.1     hwriter_1.2     MASS_7.3-13     RCurl_1.4-2
> [5] splines_2.13.1  survival_2.36-9 XML_3.1-0
>
>
>
>
>


-- 
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109

Location: M1-B861
Telephone: 206 667-2793